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FNNDSC / med2image

Converts medical images to more displayable formats, e.g. NIfTI to jpg.
MIT License
185 stars 56 forks source link

Getting this error while trying to convert #21

Open nevilpaul opened 5 years ago

nevilpaul commented 5 years ago

$ med2image -i –c0001s0004t01.nii -o input.jpg -s m C:\users\nevil\appdata\local\programs\python\python37-32\lib\site-packages\dicom__init__.py:53: UserWarning: This code is using an older version of pydicom, which is no longer maintained as of Jan 2017. You can access the new pydicom features and API by installing pydicom from PyPI. See 'Transitioning to pydicom 1.x' section at pydicom.readthedocs.org for more information.

warnings.warn(msg) usage: med2image [-h] [-i INPUTFILE] [-o OUTPUTFILESTEM] [-d OUTPUTDIR] [-t OUTPUTFILETYPE] [-s SLICETOCONVERT] [-f FRAMETOCONVERT] [--printElapsedTime] [-r] [--showSlices] [--func FUNC] [-x] [-y] [-v] med2image: error: unrecognized arguments: \x96c0001s0004t01.niiinput.jpg

yacine074 commented 4 years ago

You should change your nifti file path, just move the nifti file to another file

arushivyas commented 4 years ago

Hi, You should be passing an absolute path to the "-i" or in this case, make sure that your current working directory is the one which contains your give NIfTI volume.

For more details please refer to the: [-i|--inputFile] and [-I|--inputDir] CLI arguments in the "Command Line Arguments" section at the end of the README.rst file.

arushivyas commented 4 years ago

Please go through the new and updated README.rst file and follow the instructions to run med2image on a UNIX system.

We are now also providing a Docker container called pl-med2img

Follow this link for detailed instructions: https://github.com/FNNDSC/pl-med2img